Skip to content

Commit

Permalink
Deployed afa6e9e with MkDocs version: 1.5.3
Browse files Browse the repository at this point in the history
  • Loading branch information
@djacob65
djacob65 committed May 30, 2024
1 parent 270dea6 commit 6dba123
Show file tree
Hide file tree
Showing 10 changed files with 24 additions and 56 deletions.
2 changes: 1 addition & 1 deletion about/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -905,7 +905,7 @@ <h3 id="links">Links<a class="headerlink" href="#links" title="Permanent link">&
</ul>
<h3 id="preprint">Preprint<a class="headerlink" href="#preprint" title="Permanent link">&para;</a></h3>
<ul>
<li>D. Jacob, F. Ehrenmann, R. David, J. Tran, C. Mirande-Ney, P. Chaumeil (2024) Maggot: An ecosystem for sharing metadata within the web of <abbr title="Findable, Accessible, Interoperable and Reusable">FAIR</abbr> Data, BioRxiv, <a href="https://doi.org/10.1101/2024.05.24.595703">https://doi.org/10.1101/2024.05.24.595703</a></li>
<li>D. Jacob, F. Ehrenmann, R. David, J. Tran, C. Mirande-Ney, P. Chaumeil (2024) Maggot: An ecosystem for sharing metadata within the web of <abbr title="Findable, Accessible, Interoperable and Reusable">FAIR</abbr> Data, BioRxiv, <a href="https://doi.org/10.1101/2024.05.24.595703" target="_blank">DOI:10.1101/2024.05.24.595703</a></li>
</ul>
<h3 id="contacts">Contacts<a class="headerlink" href="#contacts" title="Permanent link">&para;</a></h3>
<ul>
Expand Down
8 changes: 4 additions & 4 deletions chats/chat1/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@



<title>chatGPT - Maggot</title>
<title>Roles in Data Management - Maggot</title>



Expand Down Expand Up @@ -135,7 +135,7 @@
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">

chatGPT
Roles in Data Management

</span>
</div>
Expand Down Expand Up @@ -750,7 +750,7 @@



<h1>chatGPT</h1>
<h1>Roles in Data Management</h1>

<h3 id="difference-between-data-manager-and-data-steward">Difference Between Data Manager and Data Steward<a class="headerlink" href="#difference-between-data-manager-and-data-steward" title="Permanent link">&para;</a></h3>
<h4 id="data-manager">Data Manager<a class="headerlink" href="#data-manager" title="Permanent link">&para;</a></h4>
Expand Down Expand Up @@ -1066,7 +1066,7 @@ <h4 id="implementation-and-monitoring">Implementation and Monitoring<a class="he
</li>
</ol>
<hr />
<p>Chat generated by chatGPT 3.5 - May 24, 2024</p>
<p><font size="-1">Generated by chatGPT 3.5 - May 24, 2024</font></p>



Expand Down
8 changes: 4 additions & 4 deletions chats/chat2/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@



<title>chatGPT - Maggot</title>
<title>Good Data Management Practices - Maggot</title>



Expand Down Expand Up @@ -135,7 +135,7 @@
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">

chatGPT
Good Data Management Practices

</span>
</div>
Expand Down Expand Up @@ -750,7 +750,7 @@



<h1>chatGPT</h1>
<h1>Good Data Management Practices</h1>

<h2 id="how-can-we-properly-respect-the-data-life-cycle-in-scientific-research-in-order-to-carry-out-good-data-management">How can we properly respect the data life cycle in scientific research in order to carry out good data management?<a class="headerlink" href="#how-can-we-properly-respect-the-data-life-cycle-in-scientific-research-in-order-to-carry-out-good-data-management" title="Permanent link">&para;</a></h2>
<p>Properly respecting the data life cycle in scientific research is crucial for effective data management. The data life cycle encompasses the stages through which data passes, from its initial generation to its eventual archiving and potential reuse. Here’s a comprehensive approach to managing the data life cycle in scientific research:</p>
Expand Down Expand Up @@ -838,7 +838,7 @@ <h3 id="7-data-archiving_1">7. Data Archiving<a class="headerlink" href="#7-data
</ul>
<p>By thoroughly documenting at these crucial stages, researchers can enhance the transparency, reproducibility, and overall quality of their data management practices.</p>
<hr />
<p>Chat generated by chatGPT 3.5 - May 24, 2024</p>
<p><font size="-1">Generated by chatGPT 3.5 - May 24, 2024</font></p>



Expand Down
8 changes: 4 additions & 4 deletions chats/chat3/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@



<title>chatGPT - Maggot</title>
<title>Controlled Vocabulary Management - Maggot</title>



Expand Down Expand Up @@ -135,7 +135,7 @@
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">

chatGPT
Controlled Vocabulary Management

</span>
</div>
Expand Down Expand Up @@ -750,7 +750,7 @@



<h1>chatGPT</h1>
<h1>Controlled Vocabulary Management</h1>

<h2 id="what-are-the-steps-to-building-our-own-controlled-vocabulary">What are the steps to building our own controlled vocabulary ?<a class="headerlink" href="#what-are-the-steps-to-building-our-own-controlled-vocabulary" title="Permanent link">&para;</a></h2>
<p>Creating a controlled vocabulary is a systematic process that involves several key steps. Here’s a detailed guide to help you build your own controlled vocabulary:</p>
Expand Down Expand Up @@ -939,7 +939,7 @@ <h3 id="example-evolution-path">Example Evolution Path<a class="headerlink" href
</ol>
<p>By following this gradual evolution, you can systematically enhance your metadata management capabilities, ensuring your system remains adaptable and meets the growing complexity of your data and user needs.</p>
<hr />
<p>Chat generated by chatGPT 3.5 - May 24, 2024</p>
<p><font size="-1">Generated by chatGPT 3.5 - May 24, 2024</font></p>



Expand Down
42 changes: 5 additions & 37 deletions chats/chat4/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@



<title>chatGPT - Maggot</title>
<title>Metadata Crosswalk - Maggot</title>



Expand Down Expand Up @@ -135,7 +135,7 @@
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">

chatGPT
Metadata Crosswalk

</span>
</div>
Expand Down Expand Up @@ -750,7 +750,7 @@



<h1>chatGPT</h1>
<h1>Metadata Crosswalk</h1>

<h3 id="what-is-metadata-crosswalk">What is metadata crosswalk?<a class="headerlink" href="#what-is-metadata-crosswalk" title="Permanent link">&para;</a></h3>
<p>A metadata crosswalk is a structured mapping between the metadata elements of two or more different systems or standards. Metadata, in this context, refers to descriptive information about data or resources, such as titles, authors, dates, keywords, etc. </p>
Expand All @@ -777,41 +777,9 @@ <h3 id="whats-the-point">What's the point ?<a class="headerlink" href="#whats-th
</li>
</ol>
<p>Overall, the point of a metadata crosswalk is to promote seamless communication, integration, and interoperability between different systems or standards, ultimately enhancing the usability and accessibility of data across diverse environments.</p>
<h3 id="can-you-suggest-some-interesting-links-on-the-subject-related-to-life-science">Can you suggest some interesting links on the subject related to life science ?<a class="headerlink" href="#can-you-suggest-some-interesting-links-on-the-subject-related-to-life-science" title="Permanent link">&para;</a></h3>
<p>Certainly! Here are some interesting links related to metadata crosswalks in the context of life sciences:</p>
<ol>
<li>
<p><strong>NCBI Metadata Crosswalk Tool</strong>:</p>
<ul>
<li>This tool provided by the National Center for Biotechnology Information (NCBI) allows users to convert metadata between various standards commonly used in life sciences, such as Dublin Core, MIAME/Minimum Information About a Microarray Experiment, and SRA/SRA Study XML.</li>
<li>Link: <a href="https://www.ncbi.nlm.nih.gov/guide/all/#sra_study" target="_blank">NCBI Metadata Crosswalk Tool</a></li>
</ul>
</li>
<li>
<p><strong>Metadata Standards and Tools for Life Sciences</strong>:</p>
<ul>
<li>This page from the European Bioinformatics Institute (EMBL-EBI) provides an overview of metadata standards commonly used in life sciences research, along with links to tools and resources for managing metadata and converting between different standards.</li>
<li>Link: <a href="https://www.ebi.ac.uk/services/all/biometa-s" target="_blank">EMBL-EBI Metadata Standards and Tools</a></li>
</ul>
</li>
<li>
<p><strong>FAIRsharing</strong>:</p>
<ul>
<li>FAIRsharing is a curated resource that provides information about standards, databases, and data policies in the life sciences and related disciplines. It includes a section specifically dedicated to metadata standards and vocabularies.</li>
<li>Link: <a href="https://fairsharing.org/standards" target="_blank">FAIRsharing Metadata Standards</a></li>
</ul>
</li>
<li>
<p><strong>NIH Common Data Elements (CDE) Repository</strong>:</p>
<ul>
<li>The NIH Common Data Elements Repository provides a standardized set of data elements and definitions for use in NIH-funded research. While not specifically focused on metadata crosswalks, it offers valuable insights into standardizing metadata across life sciences research projects.</li>
<li>Link: <a href="https://cde.nih.gov/" target="_blank">NIH CDE Repository</a></li>
</ul>
</li>
</ol>
<p>These resources should provide you with a good starting point for exploring metadata standards and tools relevant to life sciences research.</p>
<p>See more information on <a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">Schema crosswalk</a></p>
<hr />
<p>Chat generated by chatGPT 3.5 - May 24, 2024</p>
<p><font size="-1">Generated by chatGPT 3.5 - May 24, 2024</font></p>



Expand Down
2 changes: 1 addition & 1 deletion definitions/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -766,7 +766,7 @@ <h3 id="metadata-definition-files">Metadata definition files<a class="headerlink
<p>There are <strong>two levels of definition files</strong> as shown the figure below:</p>
<p><center><a href="../images/definitions_fig2.png" data-lightbox="fig2"><img src="../images/definitions_fig2.png" width="600px"></a></center></p>
<p><strong>1</strong> - The first level concerns the definition of terminology (metadata) similar to a <a href="https://sustainableheritagenetwork.org/system/files/atoms/file/How_to_Create_a_Descriptive_Metadata_Plan.pdf" target="_blank">descriptive metadata plan</a>. Clearly, this category is more akin to configuration files. They represent the heart of the application around which everything else is based. The input and search interfaces are completely generated from these definition files (especially the <em><a href="terminology">web/conf/config_terms.txt</a></em> file), thus defining each of the fields, their <a href="../images/terminology_types.png" data-lightbox="fig3">input type</a> (<em>checkbox</em>, <em>dropbox</em>, <em>textbox</em>, ...) and the associated <a href="vocabulary">controlled vocabulary</a> (ontology and thesaurus by <abbr title="feature in which an application predicts the rest of a word a user is typing">autocompletion</abbr>, drop-down list according to a list of fixed terms). This is why a <a href="../configuration">configuration step</a> is essential in order to be able to configure all the other modules.</p>
<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="dataverse">Dataverse</a>, <a href="zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="../settings/#incconfigconfiginc">Settings</a>).</p>
<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="../chats/chat4" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="dataverse">Dataverse</a>, <a href="zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="../settings/#incconfigconfiginc">Settings</a>).</p>
<p>All definition files are made using a simple spreadsheet then exported in <abbr title="Open text format representing tabular data as &quot;Tab-Separated Values&quot;. Each row corresponds to a table row and the cells in a row are separated by a tab">TSV</abbr> format. </p>
<p>The list of definition files in Maggot are given below. All must be put under the directory <em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>.
<center><a href="https://pmb-bordeaux.fr/maggot/config/view" target="_blank"><img src="../images/definitions_fig1.png" width="600px"></a></center></p>
Expand Down
6 changes: 3 additions & 3 deletions print_page/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1232,7 +1232,7 @@ <h3 id="definitions-metadata-definition-files">Metadata definition files<a class
<p>There are <strong>two levels of definition files</strong> as shown the figure below:</p>
<p><center><a href="../images/definitions_fig2.png" data-lightbox="fig2"><img src="../images/definitions_fig2.png" width="600px"></a></center></p>
<p><strong>1</strong> - The first level concerns the definition of terminology (metadata) similar to a <a href="https://sustainableheritagenetwork.org/system/files/atoms/file/How_to_Create_a_Descriptive_Metadata_Plan.pdf" target="_blank">descriptive metadata plan</a>. Clearly, this category is more akin to configuration files. They represent the heart of the application around which everything else is based. The input and search interfaces are completely generated from these definition files (especially the <em><a href="#definitions-terminology">web/conf/config_terms.txt</a></em> file), thus defining each of the fields, their <a href="../images/terminology_types.png" data-lightbox="fig3">input type</a> (<em>checkbox</em>, <em>dropbox</em>, <em>textbox</em>, ...) and the associated <a href="#definitions-vocabulary">controlled vocabulary</a> (ontology and thesaurus by <abbr title="feature in which an application predicts the rest of a word a user is typing">autocompletion</abbr>, drop-down list according to a list of fixed terms). This is why a <a href="#configuration">configuration step</a> is essential in order to be able to configure all the other modules.</p>
<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="#definitions-dataverse">Dataverse</a>, <a href="#definitions-zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="#definitions-json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="#definitions-oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="#settings-incconfigconfiginc">Settings</a>).</p>
<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="#chats-chat4" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="#definitions-dataverse">Dataverse</a>, <a href="#definitions-zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="#definitions-json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="#definitions-oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="#settings-incconfigconfiginc">Settings</a>).</p>
<p>All definition files are made using a simple spreadsheet then exported in <abbr title="Open text format representing tabular data as &quot;Tab-Separated Values&quot;. Each row corresponds to a table row and the cells in a row are separated by a tab">TSV</abbr> format. </p>
<p>The list of definition files in Maggot are given below. All must be put under the directory <em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>.
<center><a href="https://pmb-bordeaux.fr/maggot/config/view" target="_blank"><img src="../images/definitions_fig1.png" width="600px"></a></center></p>
Expand Down Expand Up @@ -1665,7 +1665,7 @@ <h3 id="publish-publish-metadata_1">Publish Metadata<a class="headerlink" href="
</center></p>
<ul>
<li>We start from the Maggot JSON format metadata file generated from the web interface and based on the metadata profile defined by the terminology definition files. </li>
<li>Then from a file defining the correspondence between the Maggot fields and those of the target repository, we can perform a <a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a> to the JSON format supported by the web API of the target repository.</li>
<li>Then from a file defining the correspondence between the Maggot fields and those of the target repository, we can perform a <a href="#chats-chat4" target="_blank">metadata crosswalk</a> to the JSON format supported by the web API of the target repository.</li>
<li>During the process we enrich the metadata with controlled vocabularies based either on dictionaries or on thesauri and/or ontologies. For the latter cases, we use the web APIs of these sources to perform the mapping (see the <a href="#definitions-mapping">definition of mapping</a>).</li>
<li>Finally, to be able to carry out the transfer i.e. the submission to the target repository (we say "push" for short), we first need to connect to the repository in order to retrieve the key (the <a href="https://www.wallarm.com/what/what-is-an-api-token-quick-guide" target="_blank">API token</a>) authorizing us to submit the dataset. This obviously assumes that we have the privileges (creation/modification rights) to do so.</li>
</ul>
Expand Down Expand Up @@ -1807,7 +1807,7 @@ <h3 id="about-links">Links<a class="headerlink" href="#about-links" title="Perma
</ul>
<h3 id="about-preprint">Preprint<a class="headerlink" href="#about-preprint" title="Permanent link">&para;</a></h3>
<ul>
<li>D. Jacob, F. Ehrenmann, R. David, J. Tran, C. Mirande-Ney, P. Chaumeil (2024) Maggot: An ecosystem for sharing metadata within the web of <abbr title="Findable, Accessible, Interoperable and Reusable">FAIR</abbr> Data, BioRxiv, <a href="https://doi.org/10.1101/2024.05.24.595703">https://doi.org/10.1101/2024.05.24.595703</a></li>
<li>D. Jacob, F. Ehrenmann, R. David, J. Tran, C. Mirande-Ney, P. Chaumeil (2024) Maggot: An ecosystem for sharing metadata within the web of <abbr title="Findable, Accessible, Interoperable and Reusable">FAIR</abbr> Data, BioRxiv, <a href="https://doi.org/10.1101/2024.05.24.595703" target="_blank">DOI:10.1101/2024.05.24.595703</a></li>
</ul>
<h3 id="about-contacts">Contacts<a class="headerlink" href="#about-contacts" title="Permanent link">&para;</a></h3>
<ul>
Expand Down
Loading

0 comments on commit 6dba123

Please sign in to comment.